Fig. 1

Mutational landscape of DDX3X, its clinical impact and the effect of DDX3X mutation/loss on proliferation, invasiveness and chemoristance in NHL cell subtypes. A A lollipop plot showing mutations in the DDX3X gene in NHL that were identified using cancer-associated genomic databases from multiple repositories (cBioPortal, ICGC, COSMIC), published literature and OncoKB. B Kaplan-Meier survival analysis of DLBCL patients with or without mutations in the DDX3X gene showing overall survival. Available data in cBioPortal are from three different cohorts - the Diffuse Large B cell Lymphoma (DFCI, Nat Med 2018; n = 127), Diffuse Large B-Cell Lymphoma (TCGA, PanCancer Atlas; n = 48), and Lymphoid Neoplasm Diffuse Large B-cell Lymphoma (TCGA, Firehose Legacy; n = 48); accessed on 14 September 2021. Patients under the the Diffuse Large B cell Lymphoma (DFCI, Nat Med 2018) cohort were treated with R-CHOP like chemotherapy, whereas treatment information for patients under the other two cohorts is not available. C A mutational lollipop plot depicting 6 different mutations identified in R/R-DLBCL patients (n = 9) using whole exome sequencing and 4 different mutations identified in unselected DLBCL patients (n = 158) using targeted sequencing of exons 8–15. D Point mutation in DDX3X (DDX3X-R475C) in U2392 cells was created using CRISPR knock-in technique and DDX3X was depleted in U2392, BJAB HuT78 and SNK1 cell lines by nucleofecting with specific shRNA or siRNA (WT, wild-type; CTL, control; Mock, non-specific siRNA). These cells were incubated with IC₅₀ concentrations (of WT cells as indicated) of vorinostat, panobinostat, trichostatin, romidepsin, stattic, WP1066, or doxorubicin for 48 h. Cell viability was accessed by the MTS-based assay. E Cells, as described in “D”, were treated with a varying combinations of vorinostat and WP1066 and their effects on cell viability were determined and tabulated in terms of “Combination Index”. F The effect of DDX3X mutation/knockdown on cell proliferation rates in U2392, HuT78 and SNK1 cells were determined by measuring cell viability using MTS-based assay at multiple time-points up to 1 week. (G) Control or DDX3X-mutant/depleted U2392, HuT78 and SNK1 cells were serum starved and allowed to transmigrate through Matrigel towards 10% human serum-enriched medium in the trans-well plates for up to 4 h. Cell migration was automatically quantified using impedance-based measurements in real-time by xCELLigence Real Time Cell Analyzer. Data represent 3 independent experiments and values in graphs are mean ± SEM. **, p < 0.01 *, p < 0.05; ns, non-significant